[R-SIG-Mac] R 3.2.2 Hangs Reading Files in El Capitan

[Jeroen Ooms]

Can you include a reproducible example? This seems to work for me as expected:

  x <- rnorm(1e8)
  saveRDS(x, tmp <- tempfile())
  file.info(tmp)$size
  y <- readRDS(tmp)
  identical(x,y)

Could be a hw issue with your disk.




On Sun, Nov 29, 2015 at 4:34 PM, Charles DiMaggio
<charles.dimaggio at gmail.com> wrote:
> Hi. After upgrading to el capitan R hangs on readRDS() and load()  for largish (say 500MB or larger) files, requiring a Force Quit of R.  I am working on a 64 GB Mac Pro machine and had no problem loading these size files prior to upgrade.  Reading and loading smaller files (1MB or less) seems to work fine. I re-installed R 3.2.2 GUI 1.66 Mavericks, XQuartz and CLT after the upgrade. Turned off SIP but experienced the same problem.
>
> I've looked over recent list posting about R behavior after upgrade to el capitan, and have not seen anything about this.  Am hoping soon-to-be-released R version 3.2.3 (Wooden Christmas-Tree) will address this weirdness, but wondering if anyone else has experienced anything similar?
>
> First few of lines of Mac Error Report below:
>
> Date/Time:       2015-11-28 15:45:00 -0500
> OS Version:      Mac OS X 10.11.1 (Build 15B42)
> Architecture:    x86_64
> Report Version:  22
>
> Command:         R
> Path:            /Applications/R.app/Contents/MacOS/R
> Version:         R 3.2.2 GUI 1.66 Mavericks build (6996)
> Parent:          launchd [1]
> PID:             563
>
> Event:           hang
> Duration:        1.70s (process was unresponsive for 25 seconds before sampling)
> Steps:           17 (100ms sampling interval)
>
> Hardware model:  MacPro6,1
> Active cpus:     8
>
> ...
>
> Heaviest stack for the main thread of the target process:
>   17  start + 1 (libdyld.dylib + 13741) [0x7fff88f2f5ad]
>   17  main + 815 (R + 5967) [0x1053e374f]
>   17  -[REngine runREPL] + 138 (R + 75578) [0x1053f473a]
>   17  run_REngineRmainloop + 295 (R + 123751) [0x105400367]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1243228) [0x10561d85c]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 675070) [0x105592cfe]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1044002) [0x1055ece22]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 674823) [0x105592c07]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1029000) [0x1055e9388]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 673910) [0x105592876]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 750621) [0x1055a541d]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1601435) [0x105674f9b]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1592422) [0x105672c66]
>   17  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1594038) [0x1056732b6]
>   14  ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1596619) [0x105673ccb]
>   7   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1595584) [0x1056738c0]
>   6   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1592773) [0x105672dc5]
>   6   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 1600194) [0x105674ac2]
>   6   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 383889) [0x10554bb91]
>   6   ??? (<56AA7B12-7A0D-3F36-8116-218A93BC3CB3> + 316653) [0x10553b4ed]
>   1   inflate + 258 (libz.1.dylib + 20735) [0x7fff9e4e30ff] (running)
>
>
> Process:         R [563]
> Path:            /Applications/R.app/Contents/MacOS/R
> Architecture:    x86_64
> Parent:          launchd [1]
> UID:             501
> Task size:       350330 pages (+14553)
> CPU Time:        1.604s
> Note:            Unresponsive for 25 seconds before sampling
> Note:            2 idle work queue threads omitted
>
>
> Cheers
>
> Charles
>
>
> Charles DiMaggio, PhD, MPH
> Director of Injury Research
> Department of Surgery
> New York University School of Medicine
> Division of Trauma, Emergency Surgery and Critical Care Surgery
> Bellevue Hosptial Center
> 462 First Avenue, NBV 15
> New York, NY 10016-9196
> Charles.Dimaggio at nyumc.org
> Office: 212.263.3202
> Mobile: 516.308.6426
>
>
>
>
>
>
>
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